====== Creating Oligonucleotides ======
Gene Designer enables two main oligonucleotide functions which can be performed in the [[ui:construct_editor | Construct Editor]]
  * Oligonucleotides can be created manually to match any segment of sequence within a construct in either direction.
  * GeneDesigner will also automatically design oligonucleotides for sequencing a construct.
     

===== Manual creation of oligonucleotides =====
  * Oligonucleotides can be created in the [[ui:workspace_pane | Workspace Pane]] of the [[ui:construct_editor | Construct Editor]]
     * Select a portion of one or both strands of the final construct sequence at the top of the sequence display
       * The Tm of the selected sequence is automatically displayed
     * Select the "Annotate" button just above the annotation grid.  You will be prompted to select a Tm annotation, an oligonucleotide or a general annotation.  You can also name the annotations.
       * If the top strand of the final construct sequence is selected the oligonucleotide is created in the forward direction.  
       * If the bottom strand is selected the oligonucleotide is created in the reverse direction.  
       * If both strands are selected, both directions are created.
{{:guide:add_oligo3.jpg}}
===== Automatic creation of oligonucleotides for sequencing =====
  * Oligonucleotides suitable for sequencing can be created for a region of the construct selected by:
     * Selecting the icons for one or more elements within the [[ui:navigation_pane | Navigation Pane]] (Not yet working in beta version)
     * Highlighting a region of the sequence 
       * by clicking on one end of the desired sequence and dragging to the other end of the selection 
       * or by clicking on one end of the desired sequence, scrolling to the other end and clicking at the other end of the selection while holding down the shift key.
     * Select "Design Sequencing Oligos" from the "Tools" tab.
  * You will then be able to choose between 
    * The best oligo in the region in the forward or reverse direction
    * Single Strand Oligos for coverage of the region
    * Double Strand Oligos for coverage of the region
  * You will also be asked to choose

=== Parameters for coverage of a region ===
   * Approximate spacing between oligonucleotides.  
   * Direction desired.

=== Parameters for sequencing oligos ===
   * Maximum, minimum and optimal  
     * Size
     * GC content
     * Tm
{{:guide:add_seq_oligo2.jpg}}
===== Naming oligonucleotides =====
  * Oligonucleotides can be named individually when created manually, or systematically when generating an oligonucleotide report.